On Mon, 29 Dec 2008, Shi Jin wrote:
> Thank you very much.
> I did
> 1. ./configure --CC=mpixlc --FC=mpixlf77 --with-batch
> --download-f-blas-lapack=1
> =================================================================================
> Since your compute nodes require use of a batch system or mpiexec you
> must:
> 1) Submit ./conftest to 1 processor of your batch system or system you are
>
> cross-compiling for; this will generate the file reconfigure.py
>
> 2) Run ./reconfigure.py (to complete the configure process).
>
> =================================================================================
> 2. mpirun -partition R001 -n 1 -mode vn -cwd $PWD -exe $PWD/conftest
> But it exited with error during the run. I see the output file
> sjin at fen1 petsc-3.0.0-p0 $ cat reconfigure.py
> #!/usr/bin/python
>
> configure_options = [
> '--with-memcmp-ok', '--sizeof_char=1',
> '--sizeof_void_p=4',
> '--sizeof_short=2',
> '--sizeof_int=4',
> '--sizeof_long=4',
> '--sizeof_long_long=8',
> '--sizeof_float=4',
> '--sizeof_double=8',
> '--sizeof_size_t=4',
> '--bits_per_byte=8',
> '--sizeof_MPI_Comm=4',
> '--sizeof_MPI_Fint=4',
> sjin at fen1 petsc-3.0.0-p0 $
>
> It is not complete and error must have happened after sizeof_MPI_Fint. The
> good news is that the sizeof(char) error is no longer there once we do the
> batch mode. I am wondering if there is a way to keep the conftest.c source
> and relevant header files (I think they are created temporarily and deleted
> after the built). This way, it would be fairly easy to figure out which part
> is having problem.
Yes- preserving conftest.c would be useful. Currently I've managed to
grab this code by introducing a compile bug into the generated code,
and then looking at configure.log [since the compile fails - configure
spits out the code into configure.log]
For eg: - the following change will do this..
asterix:/home/balay/tmp/petsc-3.0.0-p0>hg diff
diff -r 91983f07319f config/BuildSystem/config/packages/MPI.py
--- a/config/BuildSystem/config/packages/MPI.py Tue Dec 30 00:49:45 2008 -0600
+++ b/config/BuildSystem/config/packages/MPI.py Tue Dec 30 00:50:01 2008 -0600
@@ -233,7 +233,7 @@
self.framework.addBatchBody('''
{
MPI_Aint size;
- int ierr = MPI_Type_extent(%s, &size);
+ int ierr = MPI_Type_extent(%s, &size)
if(!ierr && (size != 0)) {
fprintf(output, " \'--have-mpi-%s=1\',\\n");
} else {
asterix:/home/balay/tmp/petsc-3.0.0-p0>
However it is likely the attached patch will fix this problem [it is
scheduled for the next patch update]
cd config/BuildSystem
patch -Np1 < mpi-check-cray.patch
Satish
> Please help.
> Thank you very much.
> --
> Shi Jin, PhD
>
>
> --- On Mon, 12/29/08, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> > From: Barry Smith <bsmith at mcs.anl.gov>
> > Subject: Re: Problem installing petsc on a Blue Gene/L
> > To: petsc-users at mcs.anl.gov
> > Date: Monday, December 29, 2008, 10:34 AM
> > Since the BlueGene is a batch system you need the additional
> > option --with-batch and follow
> > the directions.
> >
> > Barry
> >
> > On Dec 29, 2008, at 4:34 AM, Shi Jin wrote:
> >
> > > Hi there,
> > >
> > > I have been trying to install petsc-3.0 on a Blue
> > Gene/L system.
> > > Here is what I used to configure:
> > > ./configure --CC=blrts_xlc
> > --CFLAGS="-I/bgl/BlueLight/ppcfloor/bglsys/include
> > -qtune=440 -qarch=440d -qlist -qsource -O3
> > -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> > -lmsglayer.rts -lrts.rts -ldevices.rts"
> > --with-mpi-compilers=0 --with-fortran=0
> > >
> > > I got an error as following:
> > > TESTING: checkSizeof from
> > config.types(/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py:251)
> > >
> > *********************************************************************************
> > > UNABLE to CONFIGURE with GIVEN OPTIONS (see
> > configure.log for details):
> > >
> > ---------------------------------------------------------------------------------------
> > > Unable to determine sizeof_char
> > >
> > *********************************************************************************
> > >
> > > Here is the relevant configure.log part:
> > > TEST checkSizeof from
> > config.types(/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py:251)
> > > TESTING: checkSizeof from
> > config.types(/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py:251)
> > > Determines the size of type "typeName", and
> > defines SIZEOF_"typeName" to be the size
> > > Checking for size of type: char
> > > Pushing language C
> > > sh: blrts_xlc -c -o conftest.o
> > -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> > -qarch=440d -qlist -qsource -O3
> > -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> > -lmsglayer.rts -lrts.rts -ldevices.rts -g conftest.c
> > > Executing: blrts_xlc -c -o conftest.o
> > -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> > -qarch=440d -qlist -qsource -O3
> > -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> > -lmsglayer.rts -lrts.rts -ldevices.rts -g conftest.c
> > > sh:
> > > Pushing language C
> > > Popping language C
> > > sh: blrts_xlc -o conftest
> > -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> > -qarch=440d -qlist -qsource -O3
> > -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> > -lmsglayer.rts -lrts.rts -ldevices.rts -g conftest.o
> > > Executing: blrts_xlc -o conftest
> > -I/bgl/BlueLight/ppcfloor/bglsys/include -qtune=440
> > -qarch=440d -qlist -qsource -O3
> > -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts
> > -lmsglayer.rts -lrts.rts -ldevices.rts -g conftest.o
> > > sh:
> > > Executing: ./conftest
> > > sh: ./conftest
> > > Executing: ./conftest
> > > sh:
> > > ERROR while running executable: Could not execute
> > './conftest':
> > >
> > *********************************************************************************
> > > UNABLE to CONFIGURE with GIVEN OPTIONS (see
> > configure.log for details):
> > >
> > ---------------------------------------------------------------------------------------
> > > Unable to determine sizeof_char
> > >
> > *********************************************************************************
> > > File "./configure", line 217, in
> > petsc_configure
> > > framework.configure(out = sys.stdout)
> > > File
> > "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/framework.py",
> > line 884, in configure
> > > child.configure()
> > > File
> > "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py",
> > line 353, in configure
> > > map(lambda type: self.executeTest(self.checkSizeof,
> > type), ['char','void *', 'short',
> > 'int', 'long', 'long long',
> > 'float', 'double', 'size_t'])
> > > File
> > "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py",
> > line 353, in <lambda>
> > > map(lambda type: self.executeTest(self.checkSizeof,
> > type), ['char','void *', 'short',
> > 'int', 'long', 'long long',
> > 'float', 'double', 'size_t'])
> > > File
> > "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/base.py",
> > line 97, in executeTest
> > > ret = apply(test, args,kargs)
> > > File
> > "/gpfs/bglscratch/pi/sjin/src/petsc-3.0.0-p0/config/BuildSystem/config/types.py",
> > line 275, in checkSizeof
> > > raise RuntimeError('Unable to determine
> > '+typename)
> > >
> > > Do you know what could be my possible cause of the
> > error?
> > > I wrote a simple C test code and was able to show that
> > sizeof(char)=1. Is there a way to get the conftest.c code
> > and try it out manually?
> > > Thanks a lot.
> > >
> > > --
> > > Shi Jin, PhD
> > >
> > >
> > >
> > >
>
>
>
>
>
-------------- next part --------------
tree 1573f683f67d
parent 0d13e9fc4001
author Matt Knepley <knepley at mcs.anl.gov> 1230131724 21600
committer Matt Knepley <knepley at mcs.anl.gov> 1230131724 21600
revision 2207
branch default
Disable testing code
diff --git a/config/packages/MPI.py b/config/packages/MPI.py
--- a/config/packages/MPI.py
+++ b/config/packages/MPI.py
@@ -218,7 +218,8 @@
oldLibs = self.compilers.LIBS
self.compilers.CPPFLAGS += ' '+self.headers.toString(self.include)
self.compilers.LIBS = self.libraries.toString(self.lib)+'
'+self.compilers.LIBS
- for datatype, name in [('MPI_LONG_DOUBLE', 'long-double'),
('MPI_ENORMOUS_DOUBLE', 'enormous-double'), ('MPI_UNBELIEVABLE_DOUBLE',
'unbelievable-double')]:
+ #for datatype, name in [('MPI_LONG_DOUBLE', 'long-double'),
('MPI_ENORMOUS_DOUBLE', 'enormous-double'), ('MPI_UNBELIEVABLE_DOUBLE',
'unbelievable-double')]:
+ for datatype, name in [('MPI_LONG_DOUBLE', 'long-double')]:
if self.checkCompile('#ifdef PETSC_HAVE_STDLIB_H\n #include
<stdlib.h>\n#endif\n#include <mpi.h>\n', 'MPI_Aint size;\nint ierr =
MPI_Type_extent('+datatype+', &size);\nif(ierr || (size == 0)) exit(1);\n'):
if 'have-mpi-'+name in self.argDB:
if int(self.argDB['have-mpi-'+name]):
tree e3bac313a1d7
parent 5c1db22fa3b5
author Matt Knepley <knepley at mcs.anl.gov> 1230134339 21600
committer Matt Knepley <knepley at mcs.anl.gov> 1230134339 21600
revision 2208
branch default
Added setup/cleanup section for batch executable and made main() take arguments
- Put in MPI_Init/Finalize() for batch run
diff --git a/config/framework.py b/config/framework.py
--- a/config/framework.py
+++ b/config/framework.py
@@ -83,8 +83,10 @@
self.argDB['CPPFLAGS'] = ''
if not 'LDFLAGS' in self.argDB:
self.argDB['LDFLAGS'] = ''
+ self.batchSetup = []
self.batchIncludes = []
self.batchBodies = []
+ self.batchCleanup = []
self.batchIncludeDirs = []
self.dependencies = {}
self.configureParent = None
@@ -817,6 +819,13 @@
self.externalPackagesDir = None
return
+ def addBatchSetup(self, setup):
+ '''Add code to be run before batch tests execute'''
+ if not isinstance(setup, list):
+ setup = [setup]
+ self.batchSetup.extend(setup)
+ return
+
def addBatchInclude(self, includes):
'''Add an include or a list of includes to the batch run'''
if not isinstance(includes, list):
@@ -831,6 +840,13 @@
self.batchBodies.extend(statements)
return
+ def addBatchCleanup(self, cleanup):
+ '''Add code to be run after batch tests execute'''
+ if not isinstance(cleanup, list):
+ cleanup = [cleanup]
+ self.batchCleanup.extend(cleanup)
+ return
+
def configureBatch(self):
'''F'''
if self.batchBodies:
@@ -841,7 +857,9 @@
body = ['FILE *output = fopen("reconfigure.py","w");']
body.append('fprintf(output, "#!'+sys.executable+'\\n");')
body.append('fprintf(output, "\\nconfigure_options = [\\n");')
+ body.extend(self.batchSetup)
body.extend(self.batchBodies)
+ body.extend(self.batchCleanup)
body.append('fprintf(output, " '+repr(args)[1:-1]+'\\n]");')
driver = ['fprintf(output, "\\nif __name__ == \'__main__\':',
' import os',
@@ -856,7 +874,7 @@
oldFlags = self.compilers.CPPFLAGS
self.compilers.CPPFLAGS += ' '.join(self.batchIncludeDirs)
self.batchIncludes.insert(0, '#include <stdio.h>\n#include
<sys/types.h>\n#include <sys/stat.h>')
- if not self.checkLink('\n'.join(self.batchIncludes)+'\n',
'\n'.join(body), cleanup = 0):
+ if not self.checkLink('\n'.join(self.batchIncludes)+'\n',
'\n'.join(body), cleanup = 0, codeBegin = '\nint main(int argc, char **argv)
{\n'):
sys.exit('Unable to generate test file for
cross-compilers/batch-system\n')
self.compilers.CPPFLAGS = oldFlags
self.logClear()
diff --git a/config/packages/MPI.py b/config/packages/MPI.py
--- a/config/packages/MPI.py
+++ b/config/packages/MPI.py
@@ -46,6 +46,7 @@
# local state
self.commf2c = 0
self.commc2f = 0
+ self.needBatchMPI = 1
return
def setupHelp(self, help):
@@ -230,6 +231,10 @@
self.addDefine('HAVE_'+datatype, 1)
self.popLanguage()
else:
+ if self.needBatchMPI:
+ self.framework.addBatchSetup('if (MPI_Init(&argc, &argv));')
+ self.framework.addBatchCleanup('if (MPI_Finalize());')
+ self.needBatchMPI = 0
self.framework.addBatchInclude(['#include <stdlib.h>', '#include
<mpi.h>'])
self.framework.addBatchBody('''
{
diff -r 97d5249b8bbd config/packages/MPI.py
--- a/config/packages/MPI.py Wed Dec 24 09:58:59 2008 -0600
+++ b/config/packages/MPI.py Sat Dec 27 09:00:46 2008 -0600
@@ -238,8 +238,11 @@
self.framework.addBatchInclude(['#include <stdlib.h>', '#include
<mpi.h>'])
self.framework.addBatchBody('''
{
- MPI_Aint size;
- int ierr = MPI_Type_extent(%s, &size);
+ MPI_Aint size=0;
+ int ierr=0;
+ if (MPI_LONG_DOUBLE != MPI_DATATYPE_NULL) {
+ ierr = MPI_Type_extent(%s, &size);
+ }
if(!ierr && (size != 0)) {
fprintf(output, " \'--have-mpi-%s=1\',\\n");
} else {
